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SFI documentation
SFI documentation

Getting started

  • Start here: is SFI right for my data?
  • Installation
  • Tutorial
  • What’s new in SFI v2

User guides

  • Trajectory data
  • Running inference
  • Measurement noise and coarse sampling
  • Underdamped systems
  • Sparse model selection
  • Diagnostics
  • Building bases
  • Models and state functions
  • Particle systems
  • Simulation
  • SPDE (spatial fields) — experimental
    • Spatial field inference (SPDE)
    • Structured fields: Layout, Sectors, and Embed

Gallery

  • Gallery
    • Getting started: end-to-end inference (Ornstein–Uhlenbeck)
    • 2D limit cycle — nonlinear overdamped inference
    • Lorenz attractor — overdamped inference
    • Lotka–Volterra ecosystem — sparse network recovery
    • Experimental-data workflow template
    • Custom basis with extras — multi-experiment traps
    • Multiplicative noise — the Landauer blowtorch
    • Anisotropic diffusion tensor field
    • Van der Pol oscillator — underdamped inference
    • Velocity-dependent noise — underdamped multiplicative diffusion
    • Home ranges in a shared landscape, from noisy gappy data
    • Time-dependent forcing — protocols as extras
    • Learning a time-dependent force field — time-Fourier basis
    • Diagnostics — assessing fit quality
    • Overdamped or underdamped? Classifying dynamics from data
    • Aligning active Brownian particles — generic pairs API
    • Nonreciprocal ABPs at large scale — 3 000 particles
    • Discovering Toner–Tu hydrodynamics from agent-based flocking
    • Discovering active-nematic hydrodynamics from a bacterial swarm
    • Gray-Scott reaction-diffusion: SPDE inference
  • Advanced
    • Neural-network force field — Müller-Brown potential
    • Multi-experiment ABP inference
    • 3D flocking — underdamped multi-particle inference

Concepts & theory

  • Parametric windowed estimators — concepts
  • Parametric windowed estimators — algorithm and parameters
  • Sparse model selection — Theory & design
  • State function design

Reference

  • Physics Reference
  • API overview
  • Inference API
  • State function API
  • Bases API
  • SPDE API reference
  • Trajectory API
  • Trajectory file formats
  • Simulation API
  • Glossary

Development

  • Developer notes
  • Agent playbooks
    • Playbook — apply inference to a dataset
    • Playbook — add a feature to SFI
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